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Sample GSM672473 Query DataSets for GSM672473
Status Public on Feb 17, 2011
Title 8135_Child (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 8135
family member: Child
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Biotin
Label protocol DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual
Hybridization protocol hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640
Scan protocol images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4
Data processing CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.
Submission date Feb 10, 2011
Last update date Feb 17, 2011
Contact name Tracy Tucker
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
Platform ID GPL3720
Series (2)
GSE27216 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions

Data table
AFFX-2315060 AB 0.000203 AB -0.096109 11.946675
AFFX-2315061 BB 0.015378 BB -0.783761 11.083273
AFFX-2315062 AB 0.044339 AB -0.160942 10.117270
AFFX-2315057 BB 0.211190 BB -0.579182 9.881075
AFFX-2315058 AA 0.005720 AA 0.770769 11.879461
AFFX-2315059 AA 0.217818 AA 0.663043 10.797271
AFFX-2315063 AB 0.112042 AB -0.305791 10.509989
AFFX-2315064 AB 0.070544 AB 0.354963 10.092255
AFFX-2315065 AA 0.148227 AA 0.620221 9.749854
AFFX-2315066 AB 0.038157 AB 0.058937 10.310215
AFFX-2315067 BB 0.001835 BB -0.597812 11.027919
AFFX-2315068 AA 0.045668 AA 0.816175 10.313739
AFFX-2315069 AA 0.089960 AA 0.570982 9.838443
AFFX-2315070 AA 0.136823 AA 0.518290 9.628563
AFFX-2315071 AB 0.024422 AB -0.195646 9.924286
AFFX-2315072 AA 0.095409 AA 0.783569 10.810413
AFFX-2315073 AA 0.033644 AA 0.767508 10.290063
AFFX-2315074 BB 0.187063 BB -0.396299 9.440308
AFFX-2315075 AB 0.003592 AB 0.109537 11.530765
AFFX-2315076 BB 0.117415 BB -0.806383 10.713799

Total number of rows: 238354

Table truncated, full table size 11215 Kbytes.

Supplementary file Size Download File type/resource
GSM672473_8135_Child_Sty.CEL.gz 25.4 Mb (ftp)(http) CEL
GSM672473_8135_Child_Sty.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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